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Saturday, March 23, 2013

CDK 1.4.16: the changes, the authors, and the reviewers

Yes, quite overdue, but here's the changelog of CDK 1.4.16. This release is about bug fixing. The first CDK 1.4 release is long behind us, and the CDK project is working hard on stabilizing the 'master' branch for the first beta releases. Because this release introduced a nasty bug, you are not supposed to use this version, but the newer 1.4.17 version instead!

The list is quite long, and includes a mix of fixes (also of unit tests), improvements, and better documentation. Things to look out for include a distribution that includes the unit tests, important fixes in comparators (affecting canonical SMILES generation), used in sorting (mind the note above, and use 1.4.17!), and a fix in the output length the ProtonTotalPartialChargeDescriptor descriptor. As always, you are recommended to upgrade, but skip this version, and go immediately for 1.4.17.

The Changes

Now also has a task to create a source distrib that includes the unit tests (per user request) 26384a5

Updated comparator on AtomPlacer. The comparator now uses the built in Integer comparator. To avoid null pointer exceptions the access to the weight value is wrapped in a private method which return the minimum integer value when the weight is not set (i.e. null). 0d658df

Corrected null handling on AtomContainer 2D centre comparison. Previous if either container was null the comparator would incorrectly return '0' indicating they were equal. The method was changed to always provide a minimum Point2d when an atom container is null. This will sort all null containers lower then non-null containers. ed399df

Replaced subtraction based comparator. This comparator is unlikely to overflow but the safety of using the equalities ensures the proper behaviour of this comparator. e5b1bc6

Replaced subtraction based comparison. When the difference (which is a double) is converted to an integer the result may overflow. This overflow can occur in rare cases but would cause the comparator to be non-transitive. 425c795

Corrected canonical label sorting in the SmilesGenerator. This canonical labels are long and thus when the difference between two values is taken the result may be larger then the largest possible integer. This in rare cases cause the value to overflow and thus make the comparator non-transitive. 704280a

corrected handling of null value in the TreeNodeComparator. Previous if any node or atom were null the comparator would return '0' which is incorrect. If one is null and the other is not the objects are not equal. d7a55d3

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